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The Acolytes were a group of mutants who embraced the teachings of Magneto. Originally led by Fabian Cortez, the Acolytes sought out Magneto in his orbital base Asteroid M. Chased by S.H.I.E.L.D. agents, the Acolytes requested sanctuary. Magneto agreed, and began stockpiling nuclear weapons as a defense against an inevitable attack when his plan was opposed by the X-Men. After Magneto was injured by Wolverine, Cortez began using his powers to supposedly "heal" Magneto. While staging a retribution assault on the island nation of Genosha, which had only recently abandoned mutant slavery, the Acolytes captured multiple X-Men. Soon after, Magneto kidnapped Professor Xavier and geneticist Moira MacTaggart. An attempt to turn the captured heroes was thwarted by the remaining X-Men, who had stormed Asteroid M in order to rescue their comrades. In the ensuing clash, Cortez betrayed Magneto, leaving him to die as Asteroid M was destroyed. The Acolytes Chrome, Anne-Marie, and Delgado sacrificed their lives to safeguard Magneto as Asteroid M crash landed in the Middle East.

Cortez was subsequently revealed to be a member of the Upstarts, young mutants vying for their own leadership by killing mutants for "points." Magneto's "martyrdom" enabled Cortez to recruit more Acolytes such as Unuscione, Cargill, and the Kleinstock brothers, who attacked Our Mother of the Sacred Heart School in upstate New York in order to capture a young boy who would become a mutant in adolescence. The X-Men stopped the attack and rescued the boy, whom the Acolytes had discarded upon discovering he had Down's syndrome. Meanwhile, an embittered Magneto recruited Exodus as his new lieutenant. Magneto created Avalon, a second space station built from the remains of Cable's space station Graymalkin as well as alien Shi'ar technology that Magneto had co-opted during his time at Xavier's School. Recapturing MacTaggart, the Acolytes hid in the abandoned Mont Saint Francis monastery on the French coast.One of their own members, Neophyte, helped the X-Men rescue MacTaggart and defeat the Acolytes after discovering the truth about Cortez's betrayal of Magneto.

The Acolytes next attacked a hospital in Wantaugh, Virginia. Government sanctioned mutant team X-Factor investigated, capturing the Acolyte named Spoor. Spoor revealed the Acolytes' plans only when X-Factor member Quicksilver, Magneto's son, was present. Spoor revealed that the Acolytes' next target was the military base in Camp Hayden, Kentucky. There X-Factor drove off the Acolytes, only to discover that Camp Hayden was actually a front for a plant producing mutant-hunting Sentinel robots. After the attack on Camp Hayden, Magneto returned with Exodus, revealed Cortez's betrayal, and wrested control of the Acolytes from him., Magneto had Exodus retrieve members of the mutant team X-Force along with the brainwashed former Mutant Liberation Front members Rusty Collins and Skids for recruiting purposes. Magneto reversed their brainwashing, and they willingly joined the Acolytes in return. The others refused, escaping back to Earth.

Magneto returned to Earth during the funeral of Illyana Rasputin, a young mutant killed by the Legacy Virus. Magneto offered the mourners membership in his Acolytes. The offer was rejected by all except for the X-Man Colossus, Illyana's brother, who lost faith in Xavier's dream after his sister's death. Colossus returned with Magneto to Avalon, and the X-Men soon assaulted the base. The attack ended when Professor Xavier wiped Magneto's mind clean, reducing him to an inert state. Exodus assumed leadership of the Acolytes. Cortez resurfaced in an attempt to seize control of Genosha, taking Magneto's non-mutant granddaughter Luna as a hostage. Luna was rescued by the combined effort of the X-Men and the Avengers, including Luna's parents, Quicksilver, and the Inhuman Crystal. Cortez was apparently killed by Exodus during the rescue.

Exodus and the Acolytes returned to Avalon, where they later found the dimensionally-displaced mutant Holocaust floating in space. Rescued and reawakened, Holocaust killed the Acolytes Rusty and Milan, and confronted Exodus. The Acolyte Voght enlisted the aid of X-Men members Cyclops and Jean Grey, albeit too late to prevent Avalon's destruction. Colossus escaped with Magneto in a life-pod, while Cyclops and Jean found themselves separated, each with a group of Acolytes. Cyclops' section of Avalon crash-landed in the Australian outback. He led the Acolytes to the X-Men's former Australian base, after which the Acolytes were arrested. Later, the Magneto-clone Joseph sought the truth about his past, a search that led him to Avalon's ruins in South America. There he encountered a group of Acolytes who believed him to be their savior reborn. Meanwhile, in Antarctica, Exodus formed his own group of Acolytes and began rebuilding Avalon, intending to launch it into space. Seeking to stop this destruction, Joseph led his Acolytes against Exodus, resulting in a war between the two factions. Ultimately, Joseph convinced all assembled that he was Magneto, and ordered the Acolytes to disband.

Reforming the Acolytes once more, Exodus attacked Wundagore Mountain in search of the High Evolutionary's power-enhancing Isotope E, but he and his followers were defeated by Quicksilver and the Knights of Wundagore. Following Magneto's return, the Acolytes once again rallied to his cause and were opposed by the X-Men., Magneto was ceded control over Genosha by the United Nations after threatening to launch an electromagnetic pulse that would bring human civilization to a standstill. Cortez resurfaced and was taken back by his former lord and master, who sought to keep Cortez at arm's length. Other members of the Acolytes soon flocked to the island nation to help rebuild its economy and way of life. Some, such as Scanner, joined the Genoshan Unified Patrol defense force. Others rebelled against Magneto, and helped the township of Carrion Cove deny him access to a device that would restore his full power. The Acolytes were last seen in Genosha before an attack by Sentinels commanded by Xavier's genetic twin, Cassandra Nova, devastated the island nation. Their current whereabouts, as well as whether they still exist as a group, remain unknown.